High-performance computing and molecular dynamics

• Grant number: 21/03224-3
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• Effective date (Start): June 01, 2021
• Effective date (End): May 31, 2024
• Field of knowledge: Physical Sciences and Mathematics - Computer Science - Computer Systems
• Principal Investigator: Guido Costa Souza de Araújo
• Grantee: Oscar Samuel Cajahuaringa Macollunco
• Host Institution: Instituto de Computação (IC). Universidade Estadual de Campinas (UNICAMP). Campinas , SP, Brazil
• Associated research grant: 13/08293-7 - CCES - Center for Computational Engineering and Sciences, AP.CEPID

Abstract

Mass spectrometry is a vital tool for molecular characterization in many areas of Biochemistry analysis. Ion-Mobility Mass Spectrometry (IM-MS) CCS is an analytical (experimental) technique used to separate and identify ionized molecules moving through a drifting gas based on their mobility. In such experiments, molecules can move in a tube and bump into gas molecules. As a result, gas molecules are reflected and the combination of the resulting collision angles is used to estimate the molecule Collision Cross Section (CCS) which depends on the molecule structure. CCS can have a number of applications like determine the conformation of molecules. It can also be used to answer a number of relevant research questions like: (a) What is the real range and flexibility of cross-linkers bound to proteins?; (b) Are proteins really stable in gas phase?; and (c) What is the charge density distribution in IM-MS conditions? Mobcal is a well- known software for CCS computation. Our group at IC-UNICAMP has worked closely with members of CCES and the Chemistry Institute of UNICAMP to improve the performance of Mobcal simulation. The complexity of the simulation grows considerably high as we increase the size of the molecule. We have parallelized CCS simulation in Mobcal using OpenMP and MPI and tested it using a number of molecules from small Ubiquitin (1201 atoms) to larger polypeptide molecule (such as 5leg constituted by 18694 atoms). The results show that our approach can considerably reduce the CCS computation time. We are planning to extend Mobcal simulation with Linked-cell techniques to improve simulation speed-up, thus enabling the CCS computation of large proteins. The PD scholarship associated to this submission will initially focus in performing this extension using the OpenMP Cluster parallel programming model developed at IC-UNICAMP. This is joint collaboration with the Computing and Chemistry Institutes of UNICAMP. (AU)

Scientific publications

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

CAJAHUARINGA, SAMUEL; ANTONELLI, ALEX. Non-equilibrium free-energy calculation of phase-boundaries using LAMMPS. COMPUTATIONAL MATERIALS SCIENCE, v. 207, p. 10-pg., 2022-05-01. (13/08293-7, 15/26434-2, 17/26105-4, 10/16970-0, 16/23891-6, 19/26088-8, 21/03224-3)

CAJAHUARINGA, SAMUEL; CAETANO, DANIEL L. Z.; ZANOTTO, LEANDRO N. N.; ARAUJO, GUIDO; SKAF, MUNIR S. S.. MassCCS: A High-Performance Collision Cross-Section Software for Large Macromolecular Assemblies. JOURNAL OF CHEMICAL INFORMATION AND MODELING, v. 63, n. 11, p. 10-pg., 2023-05-15. (13/08293-7, 19/19662-0, 21/03224-3)

CAJAHUARINGA, SAMUEL; ZANOTTO, LEANDRO N.; CAETANO, DANIEL L. Z.; RIGO, SANDRO; YVIQUEL, HERVE; SKAF, MUNIR S.; ARAUJO, GUIDO; IEEE COMP SOC. Ion-Molecule Collision Cross-Section Simulation using Linked-cell and Trajectory Parallelization. 2022 IEEE 34TH INTERNATIONAL SYMPOSIUM ON COMPUTER ARCHITECTURE AND HIGH PERFORMANCE COMPUTING (SBAC-PAD 2022), v. N/A, p. 10-pg., 2022-01-01. (12/24750-6, 16/04963-6, 13/08293-7, 21/03224-3, 19/19662-0)